Pub Date : 2023-08-10DOI: 10.1109/TMBMC.2023.3304243
Akinori Kuzuya;Shin-Ichiro M. Nomura;Taro Toyota;Takashi Nakakuki;Satoshi Murata
“Molecular Cybernetics” is an emerging research field aiming the development of “Chemical AI”, artificial intelligence with memory and learning capabilities based on molecular communication. It is originated from “Molecular Robotics,” which studies molecular systems that comprise of the three basic elements of robots; Sensing, Planning, and Acting. Development of an Amoeba-type molecular robot (unicellular artificial cell,) motivated the construction of multicellular artificial cell systems mimicking nerve systems. The major challenges in molecular cybernetics are molecular communication over two lipid-bilayer compartments, amplification of molecular information in a compartment, and large deformation of the compartment triggered by molecular signal, etc. Recently reported molecular devices and systems that contributes to the realization of Chemical AI are overviewed.
{"title":"From Molecular Robotics to Molecular Cybernetics: The First Step Toward Chemical Artificial Intelligence","authors":"Akinori Kuzuya;Shin-Ichiro M. Nomura;Taro Toyota;Takashi Nakakuki;Satoshi Murata","doi":"10.1109/TMBMC.2023.3304243","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3304243","url":null,"abstract":"“Molecular Cybernetics” is an emerging research field aiming the development of “Chemical AI”, artificial intelligence with memory and learning capabilities based on molecular communication. It is originated from “Molecular Robotics,” which studies molecular systems that comprise of the three basic elements of robots; Sensing, Planning, and Acting. Development of an Amoeba-type molecular robot (unicellular artificial cell,) motivated the construction of multicellular artificial cell systems mimicking nerve systems. The major challenges in molecular cybernetics are molecular communication over two lipid-bilayer compartments, amplification of molecular information in a compartment, and large deformation of the compartment triggered by molecular signal, etc. Recently reported molecular devices and systems that contributes to the realization of Chemical AI are overviewed.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"354-363"},"PeriodicalIF":2.2,"publicationDate":"2023-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/iel7/6687308/10255331/10214301.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982995","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-08DOI: 10.1109/TMBMC.2023.3303363
Fabio Broghammer;Siwei Zhang;Thomas Wiedemann;Peter A. Hoeher
Estimating the distance between the source of a diffusive process and a receiver has a variety of applications, ranging from gas source localization at the macro-scale to molecular communication at the micro-scale. Distance information can be extracted from features of the observed particle concentration, e.g., its peak. This paper derives the Cramér-Rao lower bound (CRB) for distance estimation given the advection-diffusion model for absorbing receivers, which is the fundamental limit of any distance estimator. Furthermore, CRBs are obtained for estimators using only information about the observed peak. A maximum-likelihood estimator using the entire signal and two estimators based on peak detection are deduced. The derived CRBs are used to study the effect of channel parameters on the estimation performance. Finally, the performance of the proposed estimators is verified by comparing the root mean squared errors with their theoretical bounds in a simulation, and preliminary experimental results are presented.
{"title":"Distance Estimation From a Diffusive Process: Theoretical Limits and Experimental Results","authors":"Fabio Broghammer;Siwei Zhang;Thomas Wiedemann;Peter A. Hoeher","doi":"10.1109/TMBMC.2023.3303363","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3303363","url":null,"abstract":"Estimating the distance between the source of a diffusive process and a receiver has a variety of applications, ranging from gas source localization at the macro-scale to molecular communication at the micro-scale. Distance information can be extracted from features of the observed particle concentration, e.g., its peak. This paper derives the Cramér-Rao lower bound (CRB) for distance estimation given the advection-diffusion model for absorbing receivers, which is the fundamental limit of any distance estimator. Furthermore, CRBs are obtained for estimators using only information about the observed peak. A maximum-likelihood estimator using the entire signal and two estimators based on peak detection are deduced. The derived CRBs are used to study the effect of channel parameters on the estimation performance. Finally, the performance of the proposed estimators is verified by comparing the root mean squared errors with their theoretical bounds in a simulation, and preliminary experimental results are presented.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"312-317"},"PeriodicalIF":2.2,"publicationDate":"2023-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/iel7/6687308/10255331/10210712.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982986","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-08DOI: 10.1109/TMBMC.2023.3302798
Ajit Kumar;Akarsh Yadav;Sudhir Kumar
Localization of nanomachines is essential for optimal functionality, including optimizing transmission rates and detecting irregular cells. The sampling concentration received by the nanomachines can be used for this purpose. The localization based on received sampling concentration requires the emission time of molecules to improve the accuracy and establish synchronization among the nanomachine. In this paper, we derive the maximum likelihood estimation for localizing nanomachine in two scenarios, that is, known and unknown emission times. In contrast to the existing model, the proposed model considers a generic input (rectangular) concentration that can accommodate both non-zero emission duration and instantaneous emission, making it more practical for many applications. The model also considers multiple symbols and challenges like inter-symbol interference. Even with the rectangular input concentration, the proposed model achieves comparable individual localization performance to the impulse concentration. Additionally, the proposed model allows for joint estimation of location and emission time using correlated observations, making it a practical and generic solution for applications.
{"title":"Rectangular Concentration-Based Nanomachine Localization in Molecular Communication Networks With Unknown Emission Time","authors":"Ajit Kumar;Akarsh Yadav;Sudhir Kumar","doi":"10.1109/TMBMC.2023.3302798","DOIUrl":"10.1109/TMBMC.2023.3302798","url":null,"abstract":"Localization of nanomachines is essential for optimal functionality, including optimizing transmission rates and detecting irregular cells. The sampling concentration received by the nanomachines can be used for this purpose. The localization based on received sampling concentration requires the emission time of molecules to improve the accuracy and establish synchronization among the nanomachine. In this paper, we derive the maximum likelihood estimation for localizing nanomachine in two scenarios, that is, known and unknown emission times. In contrast to the existing model, the proposed model considers a generic input (rectangular) concentration that can accommodate both non-zero emission duration and instantaneous emission, making it more practical for many applications. The model also considers multiple symbols and challenges like inter-symbol interference. Even with the rectangular input concentration, the proposed model achieves comparable individual localization performance to the impulse concentration. Additionally, the proposed model allows for joint estimation of location and emission time using correlated observations, making it a practical and generic solution for applications.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"472-477"},"PeriodicalIF":2.2,"publicationDate":"2023-08-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79160542","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular Communication (MC) studies the transport of information encoded in signaling molecules. To date, its application field is mainly restrained to health-related uses. However, MC in plants has been gaining increasing interest. The primary transport route in plant cell-to-cell communication are Plasmodesmata (PDs), pore-like structures dotting the plant cell wall. PDs opening state is influenced by several environmental damaging factors (i.e., plant viruses), and plant cells try to restore homeostasis through defense mechanisms. In this letter, we seek to depict the complexity of plant-based communication, and we propose a simple model that proves the influence of the PDs number and opening state in the transport of information in plants.
{"title":"The Influence of Plasmodesmata Number and Opening State on Molecular Transports in Plants","authors":"Beatrice Ruzzante;Alessandro Piscopo;Svyatoslav Salo;Maurizio Magarini;Gabriele Candiani","doi":"10.1109/TMBMC.2023.3301038","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3301038","url":null,"abstract":"Molecular Communication (MC) studies the transport of information encoded in signaling molecules. To date, its application field is mainly restrained to health-related uses. However, MC in plants has been gaining increasing interest. The primary transport route in plant cell-to-cell communication are Plasmodesmata (PDs), pore-like structures dotting the plant cell wall. PDs opening state is influenced by several environmental damaging factors (i.e., plant viruses), and plant cells try to restore homeostasis through defense mechanisms. In this letter, we seek to depict the complexity of plant-based communication, and we propose a simple model that proves the influence of the PDs number and opening state in the transport of information in plants.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"329-333"},"PeriodicalIF":2.2,"publicationDate":"2023-08-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ieeexplore.ieee.org/iel7/6687308/10255331/10208114.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-01DOI: 10.1109/TMBMC.2023.3298429
Taha Sajjad;Andrew W. Eckford
Existing molecular communication systems, both theoretical and experimental, are characterized by low information rates. In this paper, inspired by time-of-flight mass spectrometry (TOFMS), we consider the design of a molecular communication system in which the channel is a vacuum and demonstrate that this method has the potential to increase achievable information rates by many orders of magnitude. We use modelling results from TOFMS to obtain arrival time distributions for accelerated ions and use them to analyze several species of ions, including hydrogen, nitrogen, argon, and benzene. We show that the achievable information rates can be increased using a velocity (Wien) filter, which reduces uncertainty in the velocity of the ions. Using a simplified communication model, we show that data rates well above 1 Gbit/s/molecule are achievable.
{"title":"High-Speed Molecular Communication in Vacuum","authors":"Taha Sajjad;Andrew W. Eckford","doi":"10.1109/TMBMC.2023.3298429","DOIUrl":"10.1109/TMBMC.2023.3298429","url":null,"abstract":"Existing molecular communication systems, both theoretical and experimental, are characterized by low information rates. In this paper, inspired by time-of-flight mass spectrometry (TOFMS), we consider the design of a molecular communication system in which the channel is a vacuum and demonstrate that this method has the potential to increase achievable information rates by many orders of magnitude. We use modelling results from TOFMS to obtain arrival time distributions for accelerated ions and use them to analyze several species of ions, including hydrogen, nitrogen, argon, and benzene. We show that the achievable information rates can be increased using a velocity (Wien) filter, which reduces uncertainty in the velocity of the ions. Using a simplified communication model, we show that data rates well above 1 Gbit/s/molecule are achievable.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 4","pages":"382-390"},"PeriodicalIF":2.2,"publicationDate":"2023-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135784881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-20DOI: 10.1109/TMBMC.2023.3297135
Jorge Torres Gómez;Pit Hofmann;Frank H. P. Fitzek;Falko Dressler
Recent molecular communication (MC) research suggests machine learning (ML) models for symbol detection, avoiding the unfeasibility of end-to-end channel models. However, ML models are applied as black boxes, lacking proof of correctness of the underlying neural networks (NNs) to detect incoming symbols. This paper studies approaches to the explainability of NNs for symbol detection in MC channels. Based on MC channel models and real testbed measurements, we generate synthesized data and train a NN model to detect of binary transmissions in MC channels. Using the local interpretable model-agnostic explanation (LIME) method and the individual conditional expectation (ICE), the findings in this paper demonstrate the analogy between the trained NN and the standard peak and slope detectors.
{"title":"Explainability of Neural Networks for Symbol Detection in Molecular Communication Channels","authors":"Jorge Torres Gómez;Pit Hofmann;Frank H. P. Fitzek;Falko Dressler","doi":"10.1109/TMBMC.2023.3297135","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3297135","url":null,"abstract":"Recent molecular communication (MC) research suggests machine learning (ML) models for symbol detection, avoiding the unfeasibility of end-to-end channel models. However, ML models are applied as black boxes, lacking proof of correctness of the underlying neural networks (NNs) to detect incoming symbols. This paper studies approaches to the explainability of NNs for symbol detection in MC channels. Based on MC channel models and real testbed measurements, we generate synthesized data and train a NN model to detect of binary transmissions in MC channels. Using the local interpretable model-agnostic explanation (LIME) method and the individual conditional expectation (ICE), the findings in this paper demonstrate the analogy between the trained NN and the standard peak and slope detectors.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"323-328"},"PeriodicalIF":2.2,"publicationDate":"2023-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-19DOI: 10.1109/TMBMC.2023.3296828
Angelika S. Thalmayer;Alisa Ladebeck;Samuel Zeising;Georg Fischer
In molecular communications, magnetic nanoparticles, which are injected into a pipe flow, are used as information carriers. Due to the parabolic shape of the velocity profile in laminar flow regimes, the speed of one particle depends on its radial position in the tube. This results in an unwanted extension of a particle pulse over the propagation time. Potential overlapping of subsequent pulses induces intersymbol interference. Only few research of the current state of the art reduces velocity dispersion directly within the propagation channel. To the best of the authors’ knowledge, this is the first paper that numerically investigates different passive obstacles which are placed directly in the channel for non-turbulent flow regimes to address the dispersion effects. These obstacles serve as decelerators, as they decelerate the fastest particles while at the same time accelerating slower particles. The results reveal that a passive decelerator can reduce the velocity dispersion in molecular communications and, thus, guarantee a more packetized pulse shortly behind the decelerator but also after some distance. Compared with different decelerators, an elliptical-shaped one showed the best results, as it inverts the velocity profile.
{"title":"Reducing Dispersion in Molecular Communications by Placing Decelerators in the Propagation Channel","authors":"Angelika S. Thalmayer;Alisa Ladebeck;Samuel Zeising;Georg Fischer","doi":"10.1109/TMBMC.2023.3296828","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3296828","url":null,"abstract":"In molecular communications, magnetic nanoparticles, which are injected into a pipe flow, are used as information carriers. Due to the parabolic shape of the velocity profile in laminar flow regimes, the speed of one particle depends on its radial position in the tube. This results in an unwanted extension of a particle pulse over the propagation time. Potential overlapping of subsequent pulses induces intersymbol interference. Only few research of the current state of the art reduces velocity dispersion directly within the propagation channel. To the best of the authors’ knowledge, this is the first paper that numerically investigates different passive obstacles which are placed directly in the channel for non-turbulent flow regimes to address the dispersion effects. These obstacles serve as decelerators, as they decelerate the fastest particles while at the same time accelerating slower particles. The results reveal that a passive decelerator can reduce the velocity dispersion in molecular communications and, thus, guarantee a more packetized pulse shortly behind the decelerator but also after some distance. Compared with different decelerators, an elliptical-shaped one showed the best results, as it inverts the velocity profile.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"334-339"},"PeriodicalIF":2.2,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-18DOI: 10.1109/TMBMC.2023.3296430
Saswati Pal;Sudip Misra;Nabiul Islam
COVID-19-induced cytokine storm, which is formed due to the excessive secretion of cytokine molecules, causes multi-organ damage and subsequently, the death of COVID-19 patients. Mesenchymal Stem Cells (MSCs) are regarded as cellular vaccines to combat the hyper-inflammatory response to cytokine storms. However, determining the required dose of MSCs to be infused within a certain time period is challenging due to the complex vascular networks and varying individual immune responses. In this work, we propose a molecular communication-based system to model the transmission, propagation, and immuno-modulatory response of MSCs to the cytokine storm. The proposed analytical model provides valuable insights into the behavior of the system and can be used as a framework for further experimental-based studies to estimate the required dose of MSCs. We analyze the varying shapes and geometries of the vascular channel on the propagation of the MSCs. We observe that the higher shear stress hinders MSC signal propagation, while lower shear stress induces propagation along the channel. Simulation results show that the MSC signal peaks in four simulation days upon administering the MSCs. Further, the results reveal that repeating the MSC infusion on alternate days is required to maintain a prolonged immuno-modulating effect on the cytokine storm.
{"title":"m-MSC: Molecular Communication-Based Analysis for Controlled MSC Treatment of Cytokine Storm","authors":"Saswati Pal;Sudip Misra;Nabiul Islam","doi":"10.1109/TMBMC.2023.3296430","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3296430","url":null,"abstract":"COVID-19-induced cytokine storm, which is formed due to the excessive secretion of cytokine molecules, causes multi-organ damage and subsequently, the death of COVID-19 patients. Mesenchymal Stem Cells (MSCs) are regarded as cellular vaccines to combat the hyper-inflammatory response to cytokine storms. However, determining the required dose of MSCs to be infused within a certain time period is challenging due to the complex vascular networks and varying individual immune responses. In this work, we propose a molecular communication-based system to model the transmission, propagation, and immuno-modulatory response of MSCs to the cytokine storm. The proposed analytical model provides valuable insights into the behavior of the system and can be used as a framework for further experimental-based studies to estimate the required dose of MSCs. We analyze the varying shapes and geometries of the vascular channel on the propagation of the MSCs. We observe that the higher shear stress hinders MSC signal propagation, while lower shear stress induces propagation along the channel. Simulation results show that the MSC signal peaks in four simulation days upon administering the MSCs. Further, the results reveal that repeating the MSC infusion on alternate days is required to maintain a prolonged immuno-modulating effect on the cytokine storm.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"286-294"},"PeriodicalIF":2.2,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982984","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-13DOI: 10.1109/TMBMC.2023.3295338
Ahmet R. Emirdagi;M. Serkan Kopuzlu;M. Okan Araz;Murat Kuscu
A key challenge in Molecular Communications (MC) is low data transmission rates, which can be addressed by channel multiplexing techniques. One way to achieve channel multiplexing in MC is to leverage the diversity of different molecule types with respect to their receptor binding characteristics, such as affinity and kinetic binding/unbinding rates. In this study, we propose a practical multiplexing scheme for MC, which is based on the diversity of ligand-receptor binding affinities. This method requires only a single type of promiscuous receptor on the receiver side, capable of interacting with multiple ligand types. We analytically derive the mean Bit Error Probability (BEP) over all multiplexed MC channels as a function of similarity among ligands in terms of their receptor affinities, the number of receptors, the number of multiplexed channels, and the ratio of concentrations encoding bit-1 and bit-0. We investigate the impact of each design parameter on the performance of multiplexed MC system.
{"title":"Affinity-Division Multiplexing for Molecular Communications With Promiscuous Ligand Receptors","authors":"Ahmet R. Emirdagi;M. Serkan Kopuzlu;M. Okan Araz;Murat Kuscu","doi":"10.1109/TMBMC.2023.3295338","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3295338","url":null,"abstract":"A key challenge in Molecular Communications (MC) is low data transmission rates, which can be addressed by channel multiplexing techniques. One way to achieve channel multiplexing in MC is to leverage the diversity of different molecule types with respect to their receptor binding characteristics, such as affinity and kinetic binding/unbinding rates. In this study, we propose a practical multiplexing scheme for MC, which is based on the diversity of ligand-receptor binding affinities. This method requires only a single type of promiscuous receptor on the receiver side, capable of interacting with multiple ligand types. We analytically derive the mean Bit Error Probability (BEP) over all multiplexed MC channels as a function of similarity among ligands in terms of their receptor affinities, the number of receptors, the number of multiplexed channels, and the ratio of concentrations encoding bit-1 and bit-0. We investigate the impact of each design parameter on the performance of multiplexed MC system.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"318-322"},"PeriodicalIF":2.2,"publicationDate":"2023-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-07-05DOI: 10.1109/TMBMC.2023.3292321
Fatih Gulec;Andrew W. Eckford
Quorum sensing (QS) mimickers can be used as an effective tool to disrupt biofilms which consist of communicating bacteria and extracellular polymeric substances (EPS). In this paper, a stochastic biofilm disruption model based on the usage of QS mimickers is proposed. A chemical reaction network (CRN) involving four different states is employed to model the biological processes during the biofilm formation and its disruption via QS mimickers. In addition, a state-based stochastic simulation algorithm is proposed to simulate this CRN. The proposed model is validated by the in vitro experimental results of Pseudomonas aeruginosa biofilm and its disruption by rosmarinic acid as the QS mimicker. Our results show that there is an uncertainty in state transitions due to the effect of the randomness in the CRN. In addition to the QS activation threshold, the presented work demonstrates that there are underlying two more thresholds for the disruption of EPS and bacteria, which provides a realistic modeling for biofilm disruption with QS mimickers.
{"title":"A Stochastic Biofilm Disruption Model Based on Quorum Sensing Mimickers","authors":"Fatih Gulec;Andrew W. Eckford","doi":"10.1109/TMBMC.2023.3292321","DOIUrl":"https://doi.org/10.1109/TMBMC.2023.3292321","url":null,"abstract":"Quorum sensing (QS) mimickers can be used as an effective tool to disrupt biofilms which consist of communicating bacteria and extracellular polymeric substances (EPS). In this paper, a stochastic biofilm disruption model based on the usage of QS mimickers is proposed. A chemical reaction network (CRN) involving four different states is employed to model the biological processes during the biofilm formation and its disruption via QS mimickers. In addition, a state-based stochastic simulation algorithm is proposed to simulate this CRN. The proposed model is validated by the in vitro experimental results of Pseudomonas aeruginosa biofilm and its disruption by rosmarinic acid as the QS mimicker. Our results show that there is an uncertainty in state transitions due to the effect of the randomness in the CRN. In addition to the QS activation threshold, the presented work demonstrates that there are underlying two more thresholds for the disruption of EPS and bacteria, which provides a realistic modeling for biofilm disruption with QS mimickers.","PeriodicalId":36530,"journal":{"name":"IEEE Transactions on Molecular, Biological, and Multi-Scale Communications","volume":"9 3","pages":"346-350"},"PeriodicalIF":2.2,"publicationDate":"2023-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"67982994","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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